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Merge pull request #636 from PatrickDeelen/master
Replaced .dat matrix with lz4 row compressed .datg matrix.
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109 changes: 109 additions & 0 deletions
109
Downstreamer/src/main/java/nl/systemsgenetics/downstreamer/io/DatToDatg.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| /* | ||
| * To change this license header, choose License Headers in Project Properties. | ||
| * To change this template file, choose Tools | Templates | ||
| * and open the template in the editor. | ||
| */ | ||
| package nl.systemsgenetics.downstreamer.io; | ||
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| import com.google.common.io.Files; | ||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.Random; | ||
| import nl.systemsgenetics.downstreamer.DownstreamerOptions; | ||
| import org.apache.commons.math3.util.Precision; | ||
| import org.apache.log4j.Logger; | ||
| import umcg.genetica.math.matrix2.DoubleMatrixDataset; | ||
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| /** | ||
| * | ||
| * @author patri | ||
| */ | ||
| public class DatToDatg { | ||
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| private static final Logger LOGGER = Logger.getLogger(DatToDatg.class); | ||
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| public static void convert(DownstreamerOptions options) throws IOException{ | ||
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| String inputMatrix = options.getGwasZscoreMatrixPath(); | ||
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| if (inputMatrix.endsWith(".dat")) { | ||
| inputMatrix = inputMatrix.substring(0, inputMatrix.length() - 4); | ||
| } | ||
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| File originalDat = new File(inputMatrix + ".dat"); | ||
| File originalRow = new File(inputMatrix + ".rows.txt"); | ||
| File originalCol = new File(inputMatrix + ".cols.txt"); | ||
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| LOGGER.info("Original " + originalDat.getAbsolutePath()); | ||
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| File workdir = new File(inputMatrix).getParentFile(); | ||
| File tmpDir = new File(workdir, "tmpdir_" + String.valueOf(Math.abs(new Random().nextInt()))); | ||
| tmpDir.mkdir(); | ||
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| LOGGER.info("Tmp dir: " + tmpDir.getAbsolutePath()); | ||
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| File originalDatTmp = new File(tmpDir, originalDat.getName()); | ||
| File originalRowTmp = new File(tmpDir, originalRow.getName()); | ||
| File originalColTmp = new File(tmpDir,originalCol.getName()); | ||
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| Files.move(originalDat, originalDatTmp); | ||
| Files.move(originalRow, originalRowTmp); | ||
| Files.move(originalCol, originalColTmp); | ||
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| DoubleMatrixDataset<String, String> data = DoubleMatrixDataset.loadDoubleBinaryData(originalDatTmp.getAbsolutePath()); | ||
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| data.saveBinary(inputMatrix); | ||
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| DoubleMatrixDataset<String, String> newData = DoubleMatrixDataset.loadDoubleBinaryData(inputMatrix); | ||
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| compareTwoMatrices(data, newData,0);//This will throw IO exception if not equal | ||
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| LOGGER.info("New file is identical to original"); | ||
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| originalDatTmp.delete(); | ||
| originalRowTmp.delete(); | ||
| originalColTmp.delete(); | ||
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| if(tmpDir.listFiles().length == 0){ | ||
| tmpDir.delete(); | ||
| } | ||
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| } | ||
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| public static void compareTwoMatrices(DoubleMatrixDataset<String, String> m1, DoubleMatrixDataset<String, String> m2) throws IOException { | ||
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| compareTwoMatrices(m1, m2, 0.00000001); | ||
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| } | ||
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| public static void compareTwoMatrices(DoubleMatrixDataset<String, String> m1, DoubleMatrixDataset<String, String> m2, double delta) throws IOException { | ||
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| if(m1.rows() != m2.rows()){ | ||
| throw new IOException("Rows not equal"); | ||
| } | ||
| if(m1.columns()!= m2.columns()){ | ||
| throw new IOException("Cols not equal"); | ||
| } | ||
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| if(!m1.getRowObjects().equals(m2.getRowObjects())){ | ||
| throw new IOException("Row names not equal"); | ||
| } | ||
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| if(!m1.getColObjects().equals(m2.getColObjects())){ | ||
| throw new IOException("Col names not equal"); | ||
| } | ||
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| for (int r = 0; r < m1.rows(); ++r) { | ||
| for (int c = 0; c < m1.columns(); ++c) { | ||
| if(!Precision.equalsIncludingNaN(m1.getElementQuick(r, c), m2.getElementQuick(r, c), delta)){ | ||
| throw new IOException("Difference at r: " + r + " c: " + c); | ||
| } | ||
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| } | ||
| } | ||
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| } | ||
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| } |
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